Sector Objects

class Sector(Object)

__copy__

def __copy__() -> "Sector"

Copy the Sector.

Returns:

• Sector - A new Sector that is a copy of the original Sector.

__deepcopy__

def __deepcopy__(memo: dict) -> "Sector"

Copy the Sector with memo.

Arguments:

• memo dict - Automatically passed parameter.

Returns:

• Sector - A new Sector that is a copy of the original Sector with memo.

EnzymeSector Objects

class EnzymeSector(Sector)

DEFAULT_MOL_MASS

mean enzymes mass E.coli [g/mol]

ActiveEnzymeSector Objects

class ActiveEnzymeSector(Sector)

DEFAULT_MOL_MASS

mean enzymes mass E.coli [g/mol]

__init__

def __init__(rxn2protein: dict, configuration: Config = Config)

summary

Arguments:

• rxn2protein dict - A dictionary with reaction ID, enzymes_dict key, value pairs for each reaction in the active_enzyme sector. The enzymes_dict contains the enzyme identifiers of the enzymes related to the specific reaction as keys, and a dict with information about the enzyme as values. The information included in this dict includes the turnover number for the forward and backward reaction (1/s), molar mass of the enzyme (mol/g), gene identifiers related to the enzyme, and with which other enzymes it forms a complex.

• configuration Config object, optional - Information about the general configuration of the model, including identifier conventions. Default is as defined in the PAModelpy.configuration script for the E.coli iML1515 model.

Example:

```
For the Parameter rxn2protein a dictionary may look like this:
{
    'R1':
        {
            'E1': {'f': forward kcat, 'b': backward kcat, 'molmass': molar mass, 'genes': ['G1', 'G2'],
                   'complex_with': 'E2'},
            'E2': {'f': forward kcat, 'b': backward kcat, 'molmass': molar mass, 'genes': ['G3', 'G4'],
                   'complex_with': 'E1'}
        }
}
```

check_kcat_values

def check_kcat_values(model, reaction, kcat)

Function to check if the kcat values provided for an enzyme are consistent with the direction of the reaction.

Arguments:

• model cobra.Model or PAModel - Model to which the kcat values should be added.

• reaction cobra.Reaction - Reaction that is catalyzed with the enzyme related to the kcats.

• kcat dict - A dictionary with the turnover values for the forward and/or backward reaction for different enzymes [/s].

Example:

Example dictionary for the kcat parameter     {'E1': {'f': forward kcat, 'b': backward kcat}}   

TransEnzymeSector Objects

class TransEnzymeSector(EnzymeSector)

DEFAULT_MOL_MASS

default E. coli ribosome molar mass [g/mol]

UnusedEnzymeSector Objects

class UnusedEnzymeSector(EnzymeSector)

DEFAULT_MOL_MASS

mean enzymes mass E.coli [g/mol]

CustomSector Objects

class CustomSector(EnzymeSector)

DEFAULT_ENZYME_MOL_MASS

mean enzymes mass E.coli [g/mol]